add lemmatizer_jar config default value

Gemfile

@@ -7,6 +7,9 @@ gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'
 gem 'redis'
 gem 'ruby-xxHash'
+gem 'request_store'
+gem 'jwt'
+gem 'addressable', '~> 2.8.0'
 
 group :development do
   gem 'minitest', '~> 4.0'
@@ -17,5 +20,5 @@ end
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
 gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development'

Gemfile.lock

@@ -1,22 +1,15 @@
-GIT
-  remote: https://github.com/ontoportal-lirmm/sparql-client.git
-  revision: fb4a89b420f8eb6dda5190a126b6c62e32c4c0c9
-  branch: master
-  specs:
-    sparql-client (1.0.1)
-      json_pure (>= 1.4)
-      net-http-persistent (= 2.9.4)
-      rdf (>= 1.0)
-
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: dd9681d91873341850df5b49a0e7b8dd87a3d252
+  revision: cd5bc312bd3acd2ff056a87a6f37b5419f3444dc
   branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
       pry
-      rdf (= 1.0.8)
+      rdf (= 3.2.11)
+      rdf-raptor
+      rdf-rdfxml
+      rdf-vocab
       redis
       rest-client
       rsolr
@@ -25,7 +18,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: fa49a53a6f14569a8ad77bcd1baa503f2380c011
+  revision: c9b8b42b09f9a734507965a9529809ea581ef58a
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -43,6 +36,16 @@ GIT
       rsolr
       rubyzip
 
+GIT
+  remote: https://github.com/ontoportal-lirmm/sparql-client.git
+  revision: aed51baf4106fd0f3d0e3f9238f0aad9406aa3f0
+  branch: master
+  specs:
+    sparql-client (1.0.1)
+      json_pure (>= 1.4)
+      net-http-persistent (= 2.9.4)
+      rdf (>= 1.0)
+
 GEM
   remote: https://rubygems.org/
   specs:
@@ -54,11 +57,12 @@ GEM
       tzinfo (~> 0.3.37)
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
+    base64 (0.2.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.5)
+    bigdecimal (3.1.6)
     builder (3.2.4)
     coderay (1.1.3)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.2.3)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     date (3.3.4)
@@ -88,14 +92,18 @@ GEM
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
     ffi (1.16.3)
+    htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
     json (2.7.1)
     json_pure (2.7.1)
+    jwt (2.8.0)
+      base64
     libxml-ruby (5.0.2)
+    link_header (0.0.8)
     logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
@@ -107,13 +115,13 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1205)
+    mime-types-data (3.2024.0206)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
-    multipart-post (2.3.0)
+    multipart-post (2.4.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.9.1)
+    net-imap (0.4.10)
       date
       net-protocol
     net-pop (0.1.2)
@@ -133,16 +141,31 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.4)
-    rack (3.0.8)
+    rack (3.0.9.1)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (10.5.0)
-    rdf (1.0.8)
-      addressable (>= 2.2)
-    redis (5.0.8)
+    rdf (3.2.11)
+      link_header (~> 0.0, >= 0.0.8)
+    rdf-raptor (3.2.0)
+      ffi (~> 1.15)
+      rdf (~> 3.2)
+    rdf-rdfxml (3.2.2)
+      builder (~> 3.2)
+      htmlentities (~> 4.3)
+      rdf (~> 3.2)
+      rdf-xsd (~> 3.2)
+    rdf-vocab (3.2.7)
+      rdf (~> 3.2, >= 3.2.4)
+    rdf-xsd (3.2.1)
+      rdf (~> 3.2)
+      rexml (~> 3.2)
+    redis (5.1.0)
       redis-client (>= 0.17.0)
-    redis-client (0.19.1)
+    redis-client (0.20.0)
       connection_pool
+    request_store (1.6.0)
+      rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -172,20 +195,22 @@ GEM
       macaddr (~> 1.0)
 
 PLATFORMS
-  ruby
-  x86_64-linux
+  x86_64-darwin-23
 
 DEPENDENCIES
+  addressable (~> 2.8.0)
   cube-ruby
   faraday (~> 1.9)
   ffi
   goo!
+  jwt
   minitest (~> 4.0)
   oj (~> 3.0)
   ontologies_linked_data!
   pry
   rake (~> 10.0)
   redis
+  request_store
   ruby-xxHash
   simplecov
   simplecov-cobertura

lib/ncbo_annotator/config.rb

@@ -33,6 +33,7 @@ def config(&block)
     @settings.annotator_redis_port       ||= 6379
     @settings.enable_recognizer_param    ||= false
     @settings.supported_recognizers      ||= [:mgrep] # :mgrep, :mallet
+    @settings.lemmatizer_jar             ||= 'lib/Lemmatizer'
     puts "(AN) >> Using ANN Redis instance at "+
       "#{@settings.annotator_redis_host}:#{@settings.annotator_redis_port}"